BN0746 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 6.9862e-05 1.1155e-03
Layer 5 1.6347e-04 9.0642e-04
Layer 3 2.3161e-04 5.1314e-02
Layer 6 7.0469e-04 2.5612e-03
Layer 2 2.2068e-03 4.6019e-02
WM 2.8462e-02 1.1448e-01
Layer 1 3.4725e-01 4.7166e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 3.0117 0.7475
SEZ6L2 Layer 5 2.7998 0.7180
FAIM2 Layer 5 2.8457 0.7141
CPLX1 Layer 5 2.7910 0.7120
APBB1 Layer 5 2.6836 0.7115
HK1 Layer 5 2.9336 0.7087
INPP5F Layer 5 2.7070 0.7081
ATP1A1 Layer 5 2.4512 0.7065
UQCRH Layer 5 2.5176 0.7062
PGRMC1 Layer 5 2.5391 0.7045
TPI1 Layer 5 2.7129 0.7044
NDRG4 Layer 5 2.8281 0.7031
TOLLIP Layer 5 2.8145 0.7010
EEF1A2 Layer 6 2.7715 0.6998
BSN Layer 5 3.0723 0.6994
RAB3A Layer 5 2.8145 0.6979
FKBP8 Layer 5 2.6602 0.6974
SKP1 Layer 5 2.3438 0.6967
RTN1 Layer 5 2.5898 0.6958
PNMA8A Layer 5 2.5273 0.6956
STX1B Layer 5 2.5088 0.6948
YWHAG Layer 5 2.5723 0.6944
SYNGR3 Layer 5 2.7910 0.6937
UBE2QL1 Layer 4 2.2422 0.6926
GNAO1 Layer 5 2.6484 0.6925
BMERB1 Layer 6 2.5215 0.6924
SNCB Layer 5 2.5566 0.6924
MGST3 Layer 4 2.4453 0.6924
RGS4 Layer 4 2.7793 0.6919
PFN2 Layer 5 2.5449 0.6919
SPRYD3 Layer 6 2.5176 0.6915
ENO2 Layer 5 2.6309 0.6912
GOT1 Layer 5 2.6250 0.6911
ATP6V1B2 Layer 5 2.9531 0.6908
YPEL3 Layer 5 2.6162 0.6900
ATP6AP1 Layer 5 2.4395 0.6896
NAP1L2 Layer 5 2.5215 0.6893
TUBB2A Layer 5 2.7793 0.6891
MTCH1 Layer 6 2.5840 0.6890
SOD1 Layer 5 2.4209 0.6888
PJA2 Layer 5 2.5215 0.6885
SERPINI1 Layer 4 2.7969 0.6877
EIF4A2 Layer 5 2.2715 0.6874
ATP6V0A1 Layer 5 2.7539 0.6868
HIGD1A Layer 5 2.6543 0.6864
PTPRN Layer 5 2.7539 0.6852
SSBP3 Layer 5 3.0254 0.6851
SYNGR1 Layer 5 2.4756 0.6851
STXBP1 Layer 6 2.8086 0.6847
CCDC85B Layer 6 2.4570 0.6845

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN0746
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN0746_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0746/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0746/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0746/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0746/report/PD/BN0746_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN0746/report/PD/BN0746_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 01:35:59
  • Number of Processes: 10
  • Spending Time: 0h 3m